AutoDock is a widely distributed community code, used by a broad base of biomedical researchers for the prediction of bio-molecular interactions. It was initially developed 17 years ago, to solve the flexible ligand- protein docking problem. In the intervening years both the AutoDock user community and the program have grown. Source code has now been freely licensed to over 4000 academic laboratories, and a variety of new applications, including protein-protein docking have been published. It is currently the world's most widely used and cited molecular docking program. Critical funding is sought to support the growing user community and to further develop AutoDock capabilities. We are proposing to extend the usefulness, usability and maintainability of AutoDock, and to enhance the interactions between the users and developers by restructuring and further development of the code utilizing contemporary software engineering practices. Our recent experience with the object-oriented high-level language Python has shown us that an agile, component-based, "language-centric" approach to software development can produce code that is easily extensible, inter-operable, maintainable, and platform independent. To attain our goals we will: 1. Fully re-design the architecture of the AutoDock Suite, utilizing an object-oriented Python-based component framework, to provide modularity, extensibility, maintainability, interoperability and portability. 2. Expand the basic capabilities of AutoDock, improving the accuracy of conformation and free energy prediction and developing effective strategies for the most common applications, such as rational drug design and virtual screening. 3. Enhance and extend the graphical user interface and visualization tools of AutoDockTools, streamlining methods for coordinate management, simulation specification and workflow control, and analysis of results. 4. Provide community support for use and enhancement of AutoDock, including simplified distribution, detailed documentation, tutorials on-site and at national conferences, and on-line user groups. Project Narrative Computer software has become a critical tool in contemporary biomedical research. AutoDock is the most widely used computer program for predicting how chemical compounds interact with biological molecules. It is currently in use in over 4000 laboratories. The goal of this proposal is to support new advances and more effective use of this program to aid scientists in their discovery and design of new pharmaceuticals and other chemical compounds to aid in medical research.